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SLC39A12 solute carrier family 39 member 12 [ Homo sapiens (human) ]

Gene ID: 221074, updated on 11-Apr-2024

Summary

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Official Symbol
SLC39A12provided by HGNC
Official Full Name
solute carrier family 39 member 12provided by HGNC
Primary source
HGNC:HGNC:20860
See related
Ensembl:ENSG00000148482 MIM:608734; AllianceGenome:HGNC:20860
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZIP12; ZIP-12; LZT-Hs8; bA570F3.1
Summary
Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A12 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Aug 2008]
Expression
Restricted expression toward brain (RPKM 9.2) See more
Orthologs
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Genomic context

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Location:
10p12.33
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (17951918..18043285)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (17971349..18062603)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (18240847..18332214)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene mannose receptor C-type 1 Neighboring gene uncharacterized LOC124902600 Neighboring gene microRNA 511 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:18270087-18271286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3111 Neighboring gene SLC39A12 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:18324740-18325329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:18325330-18325918 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:18355421-18356620 Neighboring gene MPRA-validated peak890 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr10:18424852-18425818 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11486 Neighboring gene calcium voltage-gated channel auxiliary subunit beta 2 Neighboring gene uncharacterized LOC107984213 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:18629448-18629653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3112 Neighboring gene uncharacterized LOC124902386 Neighboring gene uncharacterized LOC124902387

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Role of zinc transporter ZIP12 in susceptibility-weighted brain magnetic resonance imaging (MRI) phenotypes and mitochondrial function. Strong MD, et al. FASEB J, 2020 Sep. PMID 32716562
  2. Examination of the zinc transporter gene, SLC39A12. Bly M. Schizophr Res, 2006 Jan 31. PMID 16311021
  3. Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12). Chowanadisai W, et al. Proc Natl Acad Sci U S A, 2013 Jun 11. PMID 23716681, Free PMC Article
  4. The LZT proteins; the LIV-1 subfamily of zinc transporters. Taylor KM, et al. Biochim Biophys Acta, 2003 Apr 1. PMID 12659941
  5. Polymorphisms in mitochondrial genes and prostate cancer risk. Wang L, et al. Cancer Epidemiol Biomarkers Prev, 2008 Dec. PMID 19064571, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of zinc transporter ZIP12 in susceptibility-weighted brain magnetic resonance imaging (MRI) phenotypes and mitochondrial function.
    Title: Role of zinc transporter ZIP12 in susceptibility-weighted brain magnetic resonance imaging (MRI) phenotypes and mitochondrial function.
  2. Data indicate that the zinc transporter ZIP12 (slc39a12) is highly expressed in brain.
    Title: Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12).
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Polymorphisms in mitochondrial genes and prostate cancer risk.
  5. Examination of the zinc transporter gene, SLC39A12.
    Title: Examination of the zinc transporter gene, SLC39A12.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ30499, MGC43205, MGC51099

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables monoatomic cation:bicarbonate symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in bicarbonate transport IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular monoatomic cation homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neural tube formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neuron projection extension ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of sprouting angiogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of microtubule polymerization IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of neuron projection development IEA
Inferred from Electronic Annotation
more info
  
involved_in response to decreased oxygen levels IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in zinc ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in zinc ion import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in extracellular vesicle HDA PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc transporter ZIP12
Names
LIV-1 subfamily of ZIP zinc transporter 8
ZRT/IRT-like protein 12
solute carrier family 39 (metal ion transporter), member 12
solute carrier family 39 (zinc transporter), member 12
zinc transporter 12
zrt- and Irt-like protein 12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001145195.2 → NP_001138667.1  zinc transporter ZIP12 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001138667.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL360231, BC094700, DB469365
    Consensus CDS
    CCDS44362.1
    UniProtKB/Swiss-Prot
    B7Z2Y9, B7ZL35, C9JJL4, F5GX72, Q49AN8, Q4G0L3, Q504Y0, Q5VWV8, Q5VWV9, Q6NZY5, Q96NN4
    UniProtKB/TrEMBL
    B7Z8P9
    Related
    ENSP00000366586.2, ENST00000377369.7
    Conserved Domains (1) summary
    pfam02535
    Location:369 → 671
    Zip; ZIP Zinc transporter

  2. NM_001282733.2 → NP_001269662.1  zinc transporter ZIP12 isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the coding region compared to variant 1. The encoded isoform (3) is shorter but has the same N- and C-termini compared to isoform 1.
    Source sequence(s)
    BC035118, BC094700, BF963263, DB540352, DB545916
    Consensus CDS
    CCDS60493.1
    UniProtKB/TrEMBL
    B7Z8P9
    Related
    ENSP00000366588.3, ENST00000377371.3
    Conserved Domains (1) summary
    pfam02535
    Location:369 → 670
    Zip; ZIP Zinc transporter

  3. NM_001282734.2 → NP_001269663.1  zinc transporter ZIP12 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two exons and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AK295294, BC143551, BF963263, DB469365, DB540352, DB545916
    Consensus CDS
    CCDS60494.1
    UniProtKB/TrEMBL
    B7Z8P9
    Related
    ENSP00000440445.1, ENST00000539911.5
    Conserved Domains (1) summary
    pfam02535
    Location:235 → 537
    Zip; ZIP Zinc transporter

  4. NM_152725.4 → NP_689938.2  zinc transporter ZIP12 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. The encoded isoform (2) is shorter but has the same N- and C-termini compared to isoform 1.
    Source sequence(s)
    AK055061, AL360231, BC094700, DB469365
    Consensus CDS
    CCDS7124.1
    UniProtKB/TrEMBL
    B7Z8P9
    Related
    ENSP00000366591.4, ENST00000377374.8
    Conserved Domains (1) summary
    pfam02535
    Location:369 → 634
    Zip; ZIP Zinc transporter

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    17951918..18043285
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    17971349..18062603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q504Y0.3 GenPept UniProtKB/Swiss-Prot:Q504Y0

Gene LinkOut

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